1
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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2
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Knyazev DG, Winter L, Vogt A, Posch S, Öztürk Y, Siligan C, Goessweiner-Mohr N, Hagleitner-Ertugrul N, Koch HG, Pohl P. YidC from Escherichia coli Forms an Ion-Conducting Pore upon Activation by Ribosomes. Biomolecules 2023; 13:1774. [PMID: 38136645 PMCID: PMC10741985 DOI: 10.3390/biom13121774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The universally conserved protein YidC aids in the insertion and folding of transmembrane polypeptides. Supposedly, a charged arginine faces its hydrophobic lipid core, facilitating polypeptide sliding along YidC's surface. How the membrane barrier to other molecules may be maintained is unclear. Here, we show that the purified and reconstituted E. coli YidC forms an ion-conducting transmembrane pore upon ribosome or ribosome-nascent chain complex (RNC) binding. In contrast to monomeric YidC structures, an AlphaFold parallel YidC dimer model harbors a pore. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, single-molecule fluorescence photobleaching observations, and crosslinking experiments. In the dimeric model, the conserved arginine and other residues interacting with nascent chains point into the putative pore. This result suggests the possibility of a YidC-assisted insertion mode alternative to the insertase mechanism.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Lukas Winter
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Sandra Posch
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Yavuz Öztürk
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nikolaus Goessweiner-Mohr
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nora Hagleitner-Ertugrul
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
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3
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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4
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Polasa A, Hettige J, Immadisetty K, Moradi M. An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations. Front Mol Biosci 2022; 9:954262. [PMID: 36046607 PMCID: PMC9421054 DOI: 10.3389/fmolb.2022.954262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
YidC is a membrane protein that facilitates the insertion of newly synthesized proteins into lipid membranes. Through YidC, proteins are inserted into the lipid bilayer via the SecYEG-dependent complex. Additionally, YidC functions as a chaperone in protein folding processes. Several studies have provided evidence of its independent insertion mechanism. However, the mechanistic details of the YidC SecY-independent protein insertion mechanism remain elusive at the molecular level. This study elucidates the insertion mechanism of YidC at an atomic level through a combination of equilibrium and non-equilibrium molecular dynamics (MD) simulations. Different docking models of YidC-Pf3 in the lipid bilayer were built in this study to better understand the insertion mechanism. To conduct a complete investigation of the conformational difference between the two docking models developed, we used classical molecular dynamics simulations supplemented with a non-equilibrium technique. Our findings indicate that the YidC transmembrane (TM) groove is essential for this high-affinity interaction and that the hydrophilic nature of the YidC groove plays an important role in protein transport across the cytoplasmic membrane bilayer to the periplasmic side. At different stages of the insertion process, conformational changes in YidC’s TM domain and membrane core have a mechanistic effect on the Pf3 coat protein. Furthermore, during the insertion phase, the hydration and dehydration of the YidC’s hydrophilic groove are critical. These results demonstrate that Pf3 coat protein interactions with the membrane and YidC vary in different conformational states during the insertion process. Finally, this extensive study directly confirms that YidC functions as an independent insertase.
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Laurence MJ, Carpenter TS, Laurence TA, Coleman MA, Shelby M, Liu C. Biophysical Characterization of Membrane Proteins Embedded in Nanodiscs Using Fluorescence Correlation Spectroscopy. MEMBRANES 2022; 12:membranes12040392. [PMID: 35448362 PMCID: PMC9028781 DOI: 10.3390/membranes12040392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023]
Abstract
Proteins embedded in biological membranes perform essential functions in all organisms, serving as receptors, transporters, channels, cell adhesion molecules, and other supporting cellular roles. These membrane proteins comprise ~30% of all human proteins and are the targets of ~60% of FDA-approved drugs, yet their extensive characterization using established biochemical and biophysical methods has continued to be elusive due to challenges associated with the purification of these insoluble proteins. In response, the development of nanodisc techniques, such as nanolipoprotein particles (NLPs) and styrene maleic acid polymers (SMALPs), allowed membrane proteins to be expressed and isolated in solution as part of lipid bilayer rafts with defined, consistent nanometer sizes and compositions, thus enabling solution-based measurements. Fluorescence correlation spectroscopy (FCS) is a relatively simple yet powerful optical microscopy-based technique that yields quantitative biophysical information, such as diffusion kinetics and concentrations, about individual or interacting species in solution. Here, we first summarize current nanodisc techniques and FCS fundamentals. We then provide a focused review of studies that employed FCS in combination with nanodisc technology to investigate a handful of membrane proteins, including bacteriorhodopsin, bacterial division protein ZipA, bacterial membrane insertases SecYEG and YidC, Yersinia pestis type III secretion protein YopB, yeast cell wall stress sensor Wsc1, epidermal growth factor receptor (EGFR), ABC transporters, and several G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Matthew J. Laurence
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Timothy S. Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Ted A. Laurence
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Department of Radiation Oncology, University of California Davis, Sacramento, CA 95616, USA
| | - Megan Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
| | - Chao Liu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
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6
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Hegde RS, Keenan RJ. The mechanisms of integral membrane protein biogenesis. Nat Rev Mol Cell Biol 2022; 23:107-124. [PMID: 34556847 DOI: 10.1038/s41580-021-00413-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 02/08/2023]
Abstract
Roughly one quarter of all genes code for integral membrane proteins that are inserted into the plasma membrane of prokaryotes or the endoplasmic reticulum membrane of eukaryotes. Multiple pathways are used for the targeting and insertion of membrane proteins on the basis of their topological and biophysical characteristics. Multipass membrane proteins span the membrane multiple times and face the additional challenges of intramembrane folding. In many cases, integral membrane proteins require assembly with other proteins to form multi-subunit membrane protein complexes. Recent biochemical and structural analyses have provided considerable clarity regarding the molecular basis of membrane protein targeting and insertion, with tantalizing new insights into the poorly understood processes of multipass membrane protein biogenesis and multi-subunit protein complex assembly.
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Affiliation(s)
- Ramanujan S Hegde
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Robert J Keenan
- Gordon Center for Integrative Science, The University of Chicago, Chicago, IL, USA.
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7
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Ackermann B, Dünschede B, Pietzenuk B, Justesen BH, Krämer U, Hofmann E, Günther Pomorski T, Schünemann D. Chloroplast Ribosomes Interact With the Insertase Alb3 in the Thylakoid Membrane. FRONTIERS IN PLANT SCIENCE 2021; 12:781857. [PMID: 35003166 PMCID: PMC8733628 DOI: 10.3389/fpls.2021.781857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
Members of the Oxa1/YidC/Alb3 protein family are involved in the insertion, folding, and assembly of membrane proteins in mitochondria, bacteria, and chloroplasts. The thylakoid membrane protein Alb3 mediates the chloroplast signal recognition particle (cpSRP)-dependent posttranslational insertion of nuclear-encoded light harvesting chlorophyll a/b-binding proteins and participates in the biogenesis of plastid-encoded subunits of the photosynthetic complexes. These subunits are cotranslationally inserted into the thylakoid membrane, yet very little is known about the molecular mechanisms underlying docking of the ribosome-nascent chain complexes to the chloroplast SecY/Alb3 insertion machinery. Here, we show that nanodisc-embedded Alb3 interacts with ribosomes, while the homolog Alb4, also located in the thylakoid membrane, shows no ribosome binding. Alb3 contacts the ribosome with its C-terminal region and at least one additional binding site within its hydrophobic core region. Within the C-terminal region, two conserved motifs (motifs III and IV) are cooperatively required to enable the ribosome contact. Furthermore, our data suggest that the negatively charged C-terminus of the ribosomal subunit uL4c is involved in Alb3 binding. Phylogenetic analyses of uL4 demonstrate that this region newly evolved in the green lineage during the transition from aquatic to terrestrial life.
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Affiliation(s)
- Bernd Ackermann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Beatrix Dünschede
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bo Højen Justesen
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Department of Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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8
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Srinivasan K, Banerjee A, Baid P, Dhur A, Sengupta J. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:163-198. [PMID: 35034718 DOI: 10.1016/bs.apcsb.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
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Affiliation(s)
- Krishnamoorthi Srinivasan
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aneek Banerjee
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Baid
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ankit Dhur
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jayati Sengupta
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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9
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Davis MM, Lamichhane R, Bruce BD. Elucidating Protein Translocon Dynamics with Single-Molecule Precision. Trends Cell Biol 2021; 31:569-583. [PMID: 33865650 DOI: 10.1016/j.tcb.2021.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.
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Affiliation(s)
- Madeline M Davis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Graduate Program in Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
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10
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Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021; 12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) inherits the strategy of measurement from the effective "spectroscopic ruler" FRET and can be utilized to observe molecular behaviors with relatively high throughput at nanometer scale. The simplicity in principle and configuration of smFRET make it easy to apply and couple with other technologies to comprehensively understand single-molecule dynamics in various application scenarios. Despite its widespread application, smFRET is continuously developing and novel studies based on the advanced platforms have been done. Here, we summarize some representative examples of smFRET research of recent years to exhibit the versatility and note typical strategies to further improve the performance of smFRET measurement on different biomolecules.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yi Xing
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing 100191, China;
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
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11
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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12
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Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily. Nat Struct Mol Biol 2021; 28:234-239. [PMID: 33664512 DOI: 10.1038/s41594-021-00567-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Members of the Oxa1 superfamily perform membrane protein insertion in bacteria, the eukaryotic endoplasmic reticulum (ER), and endosymbiotic organelles. Here, we review recent structures of the three ER-resident insertases and discuss the extent to which structure and function are conserved with their bacterial counterpart YidC.
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13
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Two Signal Recognition Particle Sequences Are Present in the Amino-Terminal Domain of the C-Tailed Protein SciP. J Bacteriol 2020; 203:JB.00312-20. [PMID: 33020223 DOI: 10.1128/jb.00312-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/01/2020] [Indexed: 01/22/2023] Open
Abstract
During their synthesis, the C-tailed membrane proteins expose the membrane-spanning segment late from the ribosome and consequently can insert into the membrane only posttranslationally. However, the C-tailed type 6 secretion system (T6SS) component SciP uses the bacterial signal recognition particle (SRP) system for membrane targeting, which operates cotranslationally. Analysis of possible sequence regions in the amino-terminal part of the protein revealed two candidates that were then tested for whether they function as SRP signal peptides. Both sequences were tested positive as synthetic peptides for binding to SRP. In addition, purified ribosomes with stalled nascent chains exposing either sequence were capable of binding to SRP and SRP-FtsY complexes with high affinity. Together, the data suggest that both peptides can serve as an SRP signal sequence promoting an early membrane targeting of SciP during its synthesis. Like observed for multispanning membrane proteins, the two cytoplasmic SRP signal sequences of SciP may also facilitate a retargeting event, making the targeting more efficient.IMPORTANCE C-tail proteins are anchored in the inner membrane with a transmembrane segment at the C terminus in an N-in/C-out topology. Due to this topology, membrane insertion occurs only posttranslationally. Nevertheless, the C-tail-anchored protein SciP is targeted cotranslationally by SRP. We report here that two amino-terminal hydrophobic stretches in SciP are individually recognized by SRP and target the nascent protein to FtsY. The presence of two signal sequences may enable a retargeting mechanism, as already observed for multispanning membrane proteins, to make the posttranslational insertion of SciP by YidC more efficient.
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14
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Shelby M, Gilbile D, Grant T, Bauer W, Segelke B, He W, Evans A, Crespo N, Fischer P, Pakendorf T, Hennicke V, Hunter M, Batyuk A, Barthelmess M, Meents A, Kuhl T, Frank M, Coleman M. Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies. CRYSTALS 2020; 10. [PMID: 35686136 PMCID: PMC9175823 DOI: 10.3390/cryst10100886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
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Affiliation(s)
- M.L. Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - D. Gilbile
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - T.D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - W.J. Bauer
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - B. Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - W. He
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - A.C. Evans
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - N. Crespo
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
| | - P. Fischer
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T. Pakendorf
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - V. Hennicke
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - M.S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - A. Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - M. Barthelmess
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - A. Meents
- Center for Free-Electron Laser Science, Hamburg, Germany
| | - T.L. Kuhl
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
| | - M. Frank
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
| | - M.A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Chemical Engineering, University of California at Davis, Davis, CA, USA
- Correspondence: ; Tel: +1-925-423-7687 or ; Tel: 1-925-423-5068
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15
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Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. Protein J 2020; 38:249-261. [PMID: 30972527 DOI: 10.1007/s10930-019-09830-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein translocation and membrane integration are fundamental, conserved processes. After or during ribosomal protein synthesis, precursor proteins containing an N-terminal signal sequence are directed to a conserved membrane protein complex called the Sec translocon (also known as the Sec translocase) in the endoplasmic reticulum membrane in eukaryotic cells, or the cytoplasmic membrane in bacteria. The Sec translocon comprises the Sec61 complex in eukaryotic cells, or the SecY complex in bacteria, and mediates translocation of substrate proteins across/into the membrane. Several membrane proteins are associated with the Sec translocon. In Escherichia coli, the membrane protein YidC functions not only as a chaperone for membrane protein biogenesis along with the Sec translocon, but also as an independent membrane protein insertase. To understand the molecular mechanism underlying these dynamic processes at the membrane, high-resolution structural models of these proteins are needed. This review focuses on X-ray crystallographic analyses of the Sec translocon and YidC and discusses the structural basis for protein translocation and integration.
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Affiliation(s)
- Tomoya Tsukazaki
- Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
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16
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The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2. Sci Rep 2019; 9:14451. [PMID: 31595020 PMCID: PMC6783614 DOI: 10.1038/s41598-019-51052-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022] Open
Abstract
YidC, a bacterial member of the YidC/Alb3/Oxa1 insertase family, mediates membrane protein assembly and insertion. Cytoplasmic loops are known to have functional significance in membrane proteins such as YidC. Employing microsecond-level molecular dynamics (MD) simulations, we show that the crystallographically unresolved C2 loop plays a crucial role in the structural dynamics of Bacillus halodurans YidC2. We have modeled the C2 loop and used all- atom MD simulations to investigate the structural dynamics of YidC2 in its apo form, both with and without the C2 loop. The C2 loop was found to stabilize the entire protein and particularly the C1 region. C2 was also found to stabilize the alpha-helical character of the C-terminal region. Interestingly, the highly polar or charged lipid head groups of the simulated membranes were found to interact with and stabilize the C2 loop. These findings demonstrate that the crystallographically unresolved loops of membrane proteins could be important for the stabilization of the protein despite the apparent lack of structure, which could be due to the absence of the relevant lipids to stabilize them in crystallographic conditions.
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17
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Kater L, Frieg B, Berninghausen O, Gohlke H, Beckmann R, Kedrov A. Partially inserted nascent chain unzips the lateral gate of the Sec translocon. EMBO Rep 2019; 20:e48191. [PMID: 31379073 PMCID: PMC6776908 DOI: 10.15252/embr.201948191] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 12/25/2022] Open
Abstract
The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
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Affiliation(s)
- Lukas Kater
- Gene Center MunichLudwig‐Maximilian‐UniversityMunichGermany
| | - Benedikt Frieg
- John von Neumann Institute for ComputingJülich Supercomputing CentreInstitute for Complex Systems ‐ Structural Biochemistry (ICS‐6)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Holger Gohlke
- John von Neumann Institute for ComputingJülich Supercomputing CentreInstitute for Complex Systems ‐ Structural Biochemistry (ICS‐6)Forschungszentrum Jülich GmbHJülichGermany
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | | | - Alexej Kedrov
- Gene Center MunichLudwig‐Maximilian‐UniversityMunichGermany
- Synthetic Membrane SystemsInstitute for BiochemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
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18
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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19
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Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
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Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
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20
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Abstract
Single-molecule studies provide unprecedented details about processes that are difficult to grasp by bulk biochemical assays that yield ensemble-averaged results. One of these processes is the translocation and insertion of proteins across and into the bacterial cytoplasmic membrane. This process is facilitated by the universally conserved secretion (Sec) system, a multi-subunit membrane protein complex that consists of dissociable cytoplasmic targeting components, a molecular motor, a protein-conducting membrane pore, and accessory membrane proteins. Here, we review recent insights into the mechanisms of protein translocation and membrane protein insertion from single-molecule studies.
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Affiliation(s)
- Anne-Bart Seinen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Current affiliation: Biophysics Group, AMOLF, 1098 XG Amsterdam, Netherlands
| | - Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; and the Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
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21
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Xin Y, Zhao Y, Zheng J, Zhou H, Zhang XC, Tian C, Huang Y. Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion. FASEB J 2018; 32:2411-2421. [PMID: 29295859 DOI: 10.1096/fj.201700893rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The evolutionarily conserved YidC/Oxa1/Alb3 family of proteins represents a unique membrane protein family that facilitates the insertion, folding, and assembly of a cohort of α-helical membrane proteins in all kingdoms of life, yet its underlying mechanisms remain elusive. We report the crystal structures of the full-length Thermotoga maritima YidC (TmYidC) and the TmYidC periplasmic domain (TmPD) at a resolution of 3.8 and 2.5 Å, respectively. The crystal structure of TmPD reveals a β-supersandwich fold but with apparently shortened β strands and different connectivity, as compared to the Escherichia coli YidC (EcYidC) periplasmic domain (EcPD). TmYidC in a detergent-solubilized state also adopts a monomeric form and its conserved core domain, which consists of 2 loosely associated α-helical bundles, assemble a fold similar to that of the other YidC homologues, yet distinct from that of the archaeal YidC-like DUF106 protein. Functional analysis using in vivo photo-crosslinking experiments demonstrates that Pf3 coat protein, a Sec-independent YidC substrate, exits to the lipid bilayer laterally via one of the 2 α-helical bundle interfaces: TM3-TM5. Engineered intramolecular disulfide bonds in TmYidC, in combination with complementation assays, suggest that significant rearrangement of the 2 α-helical bundles at the top of the hydrophilic groove is critical for TmYidC function. These experiments provide a more detailed mechanical insight into YidC-mediated membrane protein biogenesis.-Xin, Y., Zhao, Y., Zheng, J., Zhou, H., Zhang, X. C., Tian, C., Huang, Y. Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion.
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Affiliation(s)
- Yanlong Xin
- National Laboratory for Physical Science at Microscale, School of Life Science, University of Science and Technology of China, Hefei, China.,National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Zhao
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiangge Zheng
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changlin Tian
- National Laboratory for Physical Science at Microscale, School of Life Science, University of Science and Technology of China, Hefei, China.,High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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22
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Baker LA, Sinnige T, Schellenberger P, de Keyzer J, Siebert CA, Driessen AJM, Baldus M, Grünewald K. Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments. Structure 2017; 26:161-170.e3. [PMID: 29249608 PMCID: PMC5758107 DOI: 10.1016/j.str.2017.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/02/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022]
Abstract
Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted systems. CryoET and ssNMR give complementary information about proteins in native membranes One sample can be prepared for both methods without the use of detergents Hybrid method shows differences between purified and native preparations of YidC Sample preparation reduces costs and time and suggests new strategy for assignment
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeanine de Keyzer
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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23
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Kedrov A, Wickles S, Crevenna AH, van der Sluis EO, Buschauer R, Berninghausen O, Lamb DC, Beckmann R. Structural Dynamics of the YidC:Ribosome Complex during Membrane Protein Biogenesis. Cell Rep 2017; 17:2943-2954. [PMID: 27974208 PMCID: PMC5186731 DOI: 10.1016/j.celrep.2016.11.059] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/26/2016] [Accepted: 11/20/2016] [Indexed: 01/30/2023] Open
Abstract
Members of the YidC/Oxa1/Alb3 family universally facilitate membrane protein biogenesis, via mechanisms that have thus far remained unclear. Here, we investigated two crucial functional aspects: the interaction of YidC with ribosome:nascent chain complexes (RNCs) and the structural dynamics of RNC-bound YidC in nanodiscs. We observed that a fully exposed nascent transmembrane domain (TMD) is required for high-affinity YidC:RNC interactions, while weaker binding may already occur at earlier stages of translation. YidC efficiently catalyzed the membrane insertion of nascent TMDs in both fluid and gel phase membranes. Cryo-electron microscopy and fluorescence analysis revealed a conformational change in YidC upon nascent chain insertion: the essential TMDs 2 and 3 of YidC were tilted, while the amphipathic helix EH1 relocated into the hydrophobic core of the membrane. We suggest that EH1 serves as a mechanical lever, facilitating a coordinated movement of YidC TMDs to trigger the release of nascent chains into the membrane.
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Affiliation(s)
- Alexej Kedrov
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany.
| | - Stephan Wickles
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Alvaro H Crevenna
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), the NanoSystems Initiative Munich (NIM), Ludwig-Maximilians-University Munich, Butenandtstrasse 11, Munich 81377, Germany
| | - Eli O van der Sluis
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Robert Buschauer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), the NanoSystems Initiative Munich (NIM), Ludwig-Maximilians-University Munich, Butenandtstrasse 11, Munich 81377, Germany; Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-University, Butenandtstrasse 5-13, Munich 81377, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, Munich 81377, Germany; Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-University, Butenandtstrasse 5-13, Munich 81377, Germany.
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24
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Rouck J, Krapf J, Roy J, Huff H, Das A. Recent advances in nanodisc technology for membrane protein studies (2012-2017). FEBS Lett 2017; 591:2057-2088. [PMID: 28581067 PMCID: PMC5751705 DOI: 10.1002/1873-3468.12706] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/26/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Historically, the main barrier to membrane protein investigations has been the tendency of membrane proteins to aggregate (due to their hydrophobic nature), in aqueous solution as well as on surfaces. The introduction of biomembrane mimetics has since stimulated momentum in the field. One such mimetic, the nanodisc (ND) system, has proved to be an exceptional system for solubilizing membrane proteins. Herein, we critically evaluate the advantages and imperfections of employing nanodiscs in biophysical and biochemical studies. Specifically, we examine the techniques that have been modified to study membrane proteins in nanodiscs. Techniques discussed here include fluorescence microscopy, solution-state/solid-state nuclear magnetic resonance, electron microscopy, small-angle X-ray scattering, and several mass spectroscopy methods. Newer techniques such as SPR, charge-sensitive optical detection, and scintillation proximity assays are also reviewed. Lastly, we cover how nanodiscs are advancing nanotechnology through nanoplasmonic biosensing, lipoprotein-nanoplatelets, and sortase-mediated labeling of nanodiscs.
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Affiliation(s)
- John Rouck
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - John Krapf
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Jahnabi Roy
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Hannah Huff
- Department of Chemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
| | - Aditi Das
- Department of Comparative Biosciences, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Department of Biochemistry, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
- Beckman Institute for Advanced Science, Division of Nutritional Sciences, Neuroscience Program and Department of Bioengineering, University of Illinois Urbana–Champaign, Urbana IL 61802, USA
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25
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Sachelaru I, Winter L, Knyazev DG, Zimmermann M, Vogt A, Kuttner R, Ollinger N, Siligan C, Pohl P, Koch HG. YidC and SecYEG form a heterotetrameric protein translocation channel. Sci Rep 2017; 7:101. [PMID: 28273911 PMCID: PMC5427846 DOI: 10.1038/s41598-017-00109-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/08/2017] [Indexed: 11/26/2022] Open
Abstract
The heterotrimeric SecYEG complex cooperates with YidC to facilitate membrane protein insertion by an unknown mechanism. Here we show that YidC contacts the interior of the SecY channel resulting in a ligand-activated and voltage-dependent complex with distinct ion channel characteristics. The SecYEG pore diameter decreases from 8 Å to only 5 Å for the YidC-SecYEG pore, indicating a reduction in channel cross-section by YidC intercalation. In the presence of a substrate, YidC relocates to the rim of the pore as indicated by increased pore diameter and loss of YidC crosslinks to the channel interior. Changing the surface charge of the pore by incorporating YidC into the channel wall increases the anion selectivity, and the accompanying change in wall hydrophobicity is liable to alter the partition of helices from the pore into the membrane. This could explain how the exit of transmembrane domains from the SecY channel is facilitated by YidC.
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Affiliation(s)
- Ilie Sachelaru
- grid.5963.9Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104 Germany ,grid.5963.9Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, 79104 Freiburg, Germany
| | - Lukas Winter
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Denis G. Knyazev
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Mirjam Zimmermann
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Andreas Vogt
- grid.5963.9Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104 Germany ,grid.5963.9Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, 79104 Freiburg, Germany ,grid.5963.9Spemann-Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Roland Kuttner
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Nicole Ollinger
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Christine Siligan
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020, Linz, Austria.
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Stefan Meier Str. 17, Freiburg, 79104, Germany. .,Spemann-Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany.
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26
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Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
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Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
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27
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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28
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Koch S, de Wit JG, Vos I, Birkner JP, Gordiichuk P, Herrmann A, van Oijen AM, Driessen AJM. Lipids Activate SecA for High Affinity Binding to the SecYEG Complex. J Biol Chem 2016; 291:22534-22543. [PMID: 27613865 DOI: 10.1074/jbc.m116.743831] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Protein translocation across the bacterial cytoplasmic membrane is an essential process catalyzed predominantly by the Sec translocase. This system consists of the membrane-embedded protein-conducting channel SecYEG, the motor ATPase SecA, and the heterotrimeric SecDFyajC membrane protein complex. Previous studies suggest that anionic lipids are essential for SecA activity and that the N terminus of SecA is capable of penetrating the lipid bilayer. The role of lipid binding, however, has remained elusive. By employing differently sized nanodiscs reconstituted with single SecYEG complexes and comprising varying amounts of lipids, we establish that SecA gains access to the SecYEG complex via a lipid-bound intermediate state, whereas acidic phospholipids allosterically activate SecA for ATP-dependent protein translocation.
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Affiliation(s)
- Sabrina Koch
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials and
| | - Janny G de Wit
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials and
| | - Iuliia Vos
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials and
| | - Jan Peter Birkner
- the Single-molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pavlo Gordiichuk
- the Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, 9747 AG, Groningen, The Netherlands, and
| | - Andreas Herrmann
- the Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, 9747 AG, Groningen, The Netherlands, and
| | - Antoine M van Oijen
- the Single-molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.,the School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Arnold J M Driessen
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials and
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29
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Zhang M, Huang R, Ackermann R, Im SC, Waskell L, Schwendeman A, Ramamoorthy A. Reconstitution of the Cytb5-CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Meng Zhang
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Rui Huang
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
| | - Rose Ackermann
- Department of Medicinal Chemistry; The Biointerfaces Institute; University of Michigan; North Campus Research Complex; Ann Arbor MI 48109 USA
| | - Sang-Choul Im
- Department of Anesthesiology; University of Michigan and VA Medical Center; Ann Arbor MI 48105 USA
| | - Lucy Waskell
- Department of Anesthesiology; University of Michigan and VA Medical Center; Ann Arbor MI 48105 USA
| | - Anna Schwendeman
- Department of Medicinal Chemistry; The Biointerfaces Institute; University of Michigan; North Campus Research Complex; Ann Arbor MI 48109 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
- Department of Chemistry; University of Michigan; Ann Arbor MI 48109-1055 USA
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30
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Zhang M, Huang R, Ackermann R, Im SC, Waskell L, Schwendeman A, Ramamoorthy A. Reconstitution of the Cytb5-CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:4497-9. [PMID: 26924779 DOI: 10.1002/anie.201600073] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 01/22/2016] [Indexed: 11/05/2022]
Abstract
Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full-length membrane-bound P450 and its redox partner cytochrome b5 (cytb5 ) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane-bound complex in model membranes renders high-resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450-cytb5 complex in peptide-based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450-cytb5 complex in the nanodisc. This is the first successful demonstration of a protein-protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane-bound protein complexes.
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Affiliation(s)
- Meng Zhang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Rui Huang
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Rose Ackermann
- Department of Medicinal Chemistry, The Biointerfaces Institute, University of Michigan, North Campus Research Complex, Ann Arbor, MI, 48109, USA
| | - Sang-Choul Im
- Department of Anesthesiology, University of Michigan and VA Medical Center, Ann Arbor, MI, 48105, USA
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and VA Medical Center, Ann Arbor, MI, 48105, USA
| | - Anna Schwendeman
- Department of Medicinal Chemistry, The Biointerfaces Institute, University of Michigan, North Campus Research Complex, Ann Arbor, MI, 48109, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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31
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Horn A, Hennig J, Ahmed YL, Stier G, Wild K, Sattler M, Sinning I. Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction. Nat Commun 2015; 6:8875. [PMID: 26568381 PMCID: PMC4660199 DOI: 10.1038/ncomms9875] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/12/2015] [Indexed: 01/21/2023] Open
Abstract
Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains. The chloroplast signal recognition particle delivers LHCPs to the thylakoid membrane by interaction of cpSRP43 with the Alb3 insertase. Here the authors decipher the specific recognition of the Alb3 C-terminal tail within the interface of two communicating chromodomains by structural biochemistry.
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Affiliation(s)
- Annemarie Horn
- Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany
| | - Janosch Hennig
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching DE-85747, Germany.,Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg D-85764, Germany
| | - Yasar L Ahmed
- Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching DE-85747, Germany.,Institute of Structural Biology, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg D-85764, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany
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32
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Xu D, Gao Y, Wang P, Ran T, Wang W. Presence of an amino acid residue at position 619 required for the function of YidC in Rhodobacter sphaeroides. Biochem Biophys Res Commun 2015; 466:267-71. [PMID: 26362178 DOI: 10.1016/j.bbrc.2015.09.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 09/05/2015] [Indexed: 11/29/2022]
Abstract
YidC, the bacterial homologous protein of Oxa1 and Alb3, could insert membrane proteins into the membrane. Rhodobacter sphaeroides is a kind of photobacteria with abundant intracytoplasmic membranes. In this study, the functions of R. sphaeroides YidC and its C-terminus were investigated in the Escherichia coli YidC gene depletion strain FTL10. The results showed that RS_YidC could complement the growth of the strain FTL10, but the RS_YidC last 5 residues (619-623, KKRKP) deletion mutant could not. Interestingly, the site-directed RS_YidC mutants of any one or all of these 5 residues were still active. The deletion mutant of the last 4 residues and even the last 4 residues deletion mutant with substitution of the Ala or Glu for Lys619 still had sufficient activity to complement the growth of the strain FTL10. These results indicated that the length of the C-terminus of Rs_YidC is more important for its function than the amino acid composition or the charges of it, and the presence of an amino acid residue at position 619 is required for Rs_YidC function in E. coli. Our result also suggests that Rs_YidC may function differently as compared to its homologs.
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Affiliation(s)
- Dongqing Xu
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yanyan Gao
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ping Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Tingting Ran
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Weiwu Wang
- Key Laboratory of Microbiological Engineering of Agricultural Environment, Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China.
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33
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 PMCID: PMC4558205 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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34
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Malhotra K, Alder NN. Advances in the use of nanoscale bilayers to study membrane protein structure and function. Biotechnol Genet Eng Rev 2015; 30:79-93. [PMID: 25023464 DOI: 10.1080/02648725.2014.921502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Within the last decade, nanoscale lipid bilayers have emerged as powerful experimental systems in the analysis of membrane proteins (MPs) for both basic and applied research. These discoidal lipid lamellae are stabilized by annuli of specially engineered amphipathic polypeptides (nanodiscs) or polymers (SMALPs/Lipodisqs®). As biomembrane mimetics, they are well suited for the reconstitution of MPs within a controlled lipid environment. Moreover, because they are water-soluble, they are amenable to solution-based biochemical and biophysical experimentation. Hence, due to their solubility, size, stability, and monodispersity, nanoscale lipid bilayers offer technical advantages over more traditional MP analytic approaches such as detergent solubilization and reconstitution into lipid vesicles. In this article, we review some of the most recent advances in the synthesis of polypeptide- and polymer-bound nanoscale lipid bilayers and their application in the study of MP structure and function.
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Affiliation(s)
- Ketan Malhotra
- a Department of Molecular and Cell Biology , University of Connecticut , Storrs , CT 06269 , USA
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35
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Geng Y, Kedrov A, Caumanns JJ, Crevenna AH, Lamb DC, Beckmann R, Driessen AJM. Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity. J Biol Chem 2015; 290:17250-61. [PMID: 26023232 DOI: 10.1074/jbc.m115.650309] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/06/2022] Open
Abstract
Members of the YidC/Oxa1/Alb3 protein family mediate membrane protein insertion, and this process is initiated by the assembly of YidC·ribosome nascent chain complexes at the inner leaflet of the lipid bilayer. The positively charged C terminus of Escherichia coli YidC plays a significant role in ribosome binding but is not the sole determinant because deletion does not completely abrogate ribosome binding. The positively charged cytosolic loops C1 and C2 of YidC may provide additional docking sites. We performed systematic sequential deletions within these cytosolic domains and studied their effect on the YidC insertase activity and interaction with translation-stalled (programmed) ribosome. Deletions within loop C1 strongly affected the activity of YidC in vivo but did not influence ribosome binding or substrate insertion, whereas loop C2 appeared to be involved in ribosome binding. Combining the latter deletion with the removal of the C terminus of YidC abolished YidC-mediated insertion. We propose that these two regions play an crucial role in the formation and stabilization of an active YidC·ribosome nascent chain complex, allowing for co-translational membrane insertion, whereas loop C1 may be involved in the downstream chaperone activity of YidC or in other protein-protein interactions.
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Affiliation(s)
- Yanping Geng
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | | | - Joseph J Caumanns
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Alvaro H Crevenna
- the Physical Chemistry, Department for Chemistry, Center for Nanoscience, the NanoSystems Initiative Munich and the Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Don C Lamb
- the Physical Chemistry, Department for Chemistry, Center for Nanoscience, the NanoSystems Initiative Munich and the Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, 81377 Munich, Germany
| | | | - Arnold J M Driessen
- From the Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, Nijenborgh 7, 9747 AG Groningen, The Netherlands,
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36
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Abstract
The YidC/Alb3/Oxa1 family functions in the insertion and folding of proteins in the bacterial cytoplasmic membrane, the chloroplast thylakoid membrane, and the mitochondrial inner membrane. All members share a conserved region composed of five transmembrane regions. These proteins mediate membrane insertion of an assorted group of proteins, ranging from respiratory subunits in the mitochondria and light-harvesting chlorophyll-binding proteins in chloroplasts to ATP synthase subunits in bacteria. This review discusses the YidC/Alb3/Oxa1 protein family as well as their function in membrane insertion and two new structures of the bacterial YidC, which suggest a mechanism for membrane insertion by this family of insertases.
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Affiliation(s)
- Seth W Hennon
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Raunak Soman
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Lu Zhu
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Ross E Dalbey
- From the Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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37
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Shimokawa-Chiba N, Kumazaki K, Tsukazaki T, Nureki O, Ito K, Chiba S. Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. Proc Natl Acad Sci U S A 2015; 112:5063-8. [PMID: 25855636 PMCID: PMC4413333 DOI: 10.1073/pnas.1423817112] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recently solved crystal structure of YidC protein suggests that it mediates membrane protein insertion by means of an intramembrane cavity rather than a transmembrane (TM) pore. This concept of protein translocation prompted us to characterize the native, membrane-integrated state of YidC with respect to the hydropathic nature of its TM region. Here, we show that the cavity-forming region of the stage III sporulation protein J (SpoIIIJ), a YidC homolog, is indeed open to the aqueous milieu of the Bacillus subtilis cells and that the overall hydrophilicity of the cavity, along with the presence of an Arg residue on several alternative sites of the cavity surface, is functionally important. We propose that YidC functions as a proteinaceous amphiphile that interacts with newly synthesized membrane proteins and reduces energetic costs of their membrane traversal.
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Affiliation(s)
- Naomi Shimokawa-Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Kaoru Kumazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tomoya Tsukazaki
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; and Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koreaki Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan;
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38
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Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci Rep 2014; 4:7299. [PMID: 25466392 PMCID: PMC4252904 DOI: 10.1038/srep07299] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/17/2014] [Indexed: 11/08/2022] Open
Abstract
Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.
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Chen Y, Soman R, Shanmugam SK, Kuhn A, Dalbey RE. The role of the strictly conserved positively charged residue differs among the Gram-positive, Gram-negative, and chloroplast YidC homologs. J Biol Chem 2014; 289:35656-67. [PMID: 25359772 DOI: 10.1074/jbc.m114.595082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, the structure of YidC2 from Bacillus halodurans revealed that the conserved positively charged residue within transmembrane segment one (at position 72) is located in a hydrophilic groove that is embedded in the inner leaflet of the lipid bilayer. The arginine residue was essential for the Bacillus subtilis SpoIIIJ (YidC1) to insert MifM and to complement a SpoIIIJ mutant strain. Here, we investigated the importance of the conserved positively charged residue for the function of the Escherichia coli YidC, Streptococcus mutans YidC2, and the chloroplast Arabidopsis thaliana Alb3. Like the Gram-positive B. subtilis SpoIIIJ, the conserved arginine was required for functioning of the Gram-positive S. mutans YidC2 and was necessary to complement the E. coli YidC depletion strain and to promote insertion of a YidC-dependent membrane protein synthesized with one but not two hydrophobic segments. In contrast, the conserved positively charged residue was not required for the E. coli YidC or the A. thaliana Alb3 to functionally complement the E. coli YidC depletion strain or to promote insertion of YidC-dependent membrane proteins. Our results also show that the C-terminal half of the helical hairpin structure in cytoplasmic loop C1 is important for the activity of YidC because various deletions in the region either eliminate or impair YidC function. The results here underscore the importance of the cytoplasmic hairpin region for YidC and show that the arginine is critical for the tested Gram-positive YidC homolog but is not essential for the tested Gram-negative and chloroplast YidC homologs.
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Affiliation(s)
- Yuanyuan Chen
- From the Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 and
| | - Raunak Soman
- From the Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 and
| | - Sri Karthika Shanmugam
- From the Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 and
| | - Andreas Kuhn
- the Institute of Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Ross E Dalbey
- From the Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210 and
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Cymer F, von Heijne G, White SH. Mechanisms of integral membrane protein insertion and folding. J Mol Biol 2014; 427:999-1022. [PMID: 25277655 DOI: 10.1016/j.jmb.2014.09.014] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/13/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
The biogenesis, folding, and structure of α-helical membrane proteins (MPs) are important to understand because they underlie virtually all physiological processes in cells including key metabolic pathways, such as the respiratory chain and the photosystems, as well as the transport of solutes and signals across membranes. Nearly all MPs require translocons--often referred to as protein-conducting channels--for proper insertion into their target membrane. Remarkable progress toward understanding the structure and functioning of translocons has been made during the past decade. Here, we review and assess this progress critically. All available evidence indicates that MPs are equilibrium structures that achieve their final structural states by folding along thermodynamically controlled pathways. The main challenge for cells is the targeting and membrane insertion of highly hydrophobic amino acid sequences. Targeting and insertion are managed in cells principally by interactions between ribosomes and membrane-embedded translocons. Our review examines the biophysical and biological boundaries of MP insertion and the folding of polytopic MPs in vivo. A theme of the review is the under-appreciated role of basic thermodynamic principles in MP folding and assembly. Thermodynamics not only dictates the final folded structure but also is the driving force for the evolution of the ribosome-translocon system of assembly. We conclude the review with a perspective suggesting a new view of translocon-guided MP insertion.
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Affiliation(s)
- Florian Cymer
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm.,Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden
| | - Stephen H White
- Department of Physiology and Biophysics and the Center for Biomembrane Systems University of California, Irvine Irvine, CA 92697
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Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R. A structural model of the active ribosome-bound membrane protein insertase YidC. eLife 2014; 3:e03035. [PMID: 25012291 PMCID: PMC4124156 DOI: 10.7554/elife.03035] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.
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Affiliation(s)
- Stephan Wickles
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Jessica Andreani
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Seemayer
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas Bischoff
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Soeding
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Eli O van der Sluis
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany Center for Integrated Protein Science Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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Hennon SW, Dalbey RE. Cross-Linking-Based Flexibility and Proximity Relationships between the TM Segments of the Escherichia coli YidC. Biochemistry 2014; 53:3278-86. [DOI: 10.1021/bi500257u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seth W. Hennon
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross E. Dalbey
- Department of Chemistry and
Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama KI, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, Tsukazaki T, Nureki O. Structural basis of Sec-independent membrane protein insertion by YidC. Nature 2014; 509:516-20. [PMID: 24739968 DOI: 10.1038/nature13167] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 02/24/2014] [Indexed: 11/09/2022]
Abstract
Newly synthesized membrane proteins must be accurately inserted into the membrane, folded and assembled for proper functioning. The protein YidC inserts its substrates into the membrane, thereby facilitating membrane protein assembly in bacteria; the homologous proteins Oxa1 and Alb3 have the same function in mitochondria and chloroplasts, respectively. In the bacterial cytoplasmic membrane, YidC functions as an independent insertase and a membrane chaperone in cooperation with the translocon SecYEG. Here we present the crystal structure of YidC from Bacillus halodurans, at 2.4 Å resolution. The structure reveals a novel fold, in which five conserved transmembrane helices form a positively charged hydrophilic groove that is open towards both the lipid bilayer and the cytoplasm but closed on the extracellular side. Structure-based in vivo analyses reveal that a conserved arginine residue in the groove is important for the insertion of membrane proteins by YidC. We propose an insertion mechanism for single-spanning membrane proteins, in which the hydrophilic environment generated by the groove recruits the extracellular regions of substrates into the low-dielectric environment of the membrane.
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Affiliation(s)
- Kaoru Kumazaki
- 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan [3]
| | - Shinobu Chiba
- 1] Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan [2]
| | - Mizuki Takemoto
- 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Arata Furukawa
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Ken-ichi Nishiyama
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yasunori Sugano
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Andrés D Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yoshiki Tanaka
- Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Hiroyuki Mori
- Institute for Virus Research, Kyoto University, Shogoin Kawara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Fumio Arisaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Koreaki Ito
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Ryuichiro Ishitani
- 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Tomoya Tsukazaki
- 1] Department of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan [2] JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Osamu Nureki
- 1] Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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Dalbey RE, Kuhn A, Zhu L, Kiefer D. The membrane insertase YidC. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1489-96. [PMID: 24418623 DOI: 10.1016/j.bbamcr.2013.12.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/19/2013] [Accepted: 12/31/2013] [Indexed: 12/28/2022]
Abstract
The membrane insertases YidC-Oxa1-Alb3 provide a simple cellular system that catalyzes the transmembrane topology of newly synthesized membrane proteins. The insertases are composed of a single protein with 5 to 6 transmembrane (TM) helices that contact hydrophobic segments of the substrate proteins. Since YidC also cooperates with the Sec translocase it is widely involved in the assembly of many different membrane proteins including proteins that obtain complex membrane topologies. Homologues found in mitochondria (Oxa1) and thylakoids (Alb3) point to a common evolutionary origin and also demonstrate the general importance of this cellular process. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
| | - Andreas Kuhn
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany.
| | - Lu Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Doro Kiefer
- Institute of Microbiology and Molecular Biology, University of Hohenheim, Garbenstr 30, 70599 Stuttgart, Germany
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Taufik I, Kedrov A, Exterkate M, Driessen AJ. Monitoring the Activity of Single Translocons. J Mol Biol 2013; 425:4145-53. [DOI: 10.1016/j.jmb.2013.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
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46
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Saraogi I, Shan SO. Co-translational protein targeting to the bacterial membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1433-41. [PMID: 24513458 DOI: 10.1016/j.bbamcr.2013.10.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
Co-translational protein targeting by the Signal Recognition Particle (SRP) is an essential cellular pathway that couples the synthesis of nascent proteins to their proper cellular localization. The bacterial SRP, which contains the minimal ribonucleoprotein core of this universally conserved targeting machine, has served as a paradigm for understanding the molecular basis of protein localization in all cells. In this review, we highlight recent biochemical and structural insights into the molecular mechanisms by which fundamental challenges faced by protein targeting machineries are met in the SRP pathway. Collectively, these studies elucidate how an essential SRP RNA and two regulatory GTPases in the SRP and SRP receptor (SR) enable this targeting machinery to recognize, sense and respond to its biological effectors, i.e. the cargo protein, the target membrane and the translocation machinery, thus driving efficient and faithful co-translational protein targeting. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Ishu Saraogi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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47
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Herrmann JM. The bacterial membrane insertase YidC is a functional monomer and binds ribosomes in a nascent chain-dependent manner. J Mol Biol 2013; 425:4071-3. [PMID: 23933056 DOI: 10.1016/j.jmb.2013.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany.
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